Biomedical imaging of bacteria and viruses

Abstract

The invention relates to a non-invasive imaging method of bacteria. One embodiment comprises labeling the bacteria with a radioisotope, then delivering it to the gut of a human or animal. Another embodiment is to label bacteriophages, then administer them to a human or animal, so that they infect (and thus co-localize with) bacteria already resident in the human or animal. The bacteriophage can then be imaged, showing the location of the resident bacteria of interest. In another embodiment, the invention is related more generally to the labelling of bacteria or bacteriophages with a radio-metal or radioisotope to render the labeled gut bacteria and the bacteria in the body visible to nuclear medicine PET and SPECT imaging guided by functional/structural MRI and/or CT imaging. In another embodiment, the invention is related more generally to the labelling of bacteria or bacteriophages (both or just one) with a radio-metal or radioisotope to render the gut bacteria and the bacteria in the body visible to nuclear medicine PET and SPECT imaging guided by functional/structural MRI and/or CT imaging or visible by MRI alone or in combination with either PET or SPECT.

We claim: 
     
         1 . A method of imaging microbiota in a subject, the method comprising:
 labelling bacteria or bacteriophage with a radioisotope;   introducing the radioisotope labelled bacteria or bacteriophage into the subject; and   functionally and/or structurally imaging the subject.   
     
     
         2 . (canceled) 
     
     
         3 . The method of  claim 1 , wherein the bacteria or bacteriophage are gut bacteria or gut bacteriophage. 
     
     
         4 . The method of  claim 3 , further comprising isolating the gut bacteria or gut bacteriophage from fecal material from the subject prior to labelling. 
     
     
         5 . The method of  claim 3 , wherein gut bacteria are labelled and the gut bacteria comprise  Lactobacillus crispatus  ATCC33820. 
     
     
         6 . The method of  claim 3 , further comprising mixing the radioisotope labelled gut bacteria or gut bacteriophage into fecal material prior to its introduction into the subject. 
     
     
         7 . The method of  claim 1 , wherein the introducing of the radioisotope labelled bacteria or bacteriophage comprises ingestion of the radioisotope labelled bacteria or bacteriophage by the subject or administering the radioisotope labelled bacteria or bacteriophage into the subject by way of intravenous, intraarterial, intrathecal, intramuscular, intradermal, subcutaneous, or intracavitary administration. 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 1 , wherein the radioisotope is  89 Zr,  64 Cu,  52 Mn,  111 In,  177 Lu, or  225 Ac. 
     
     
         10 . The method of  claim 9 , wherein the radioisotope is  89 Zr and the bacteria or bacteriophage are labelled with a labelling agent comprising  89 Zr-desferrioxamine-NCS ( 89 Zr-DBN). 
     
     
         11 . (canceled) 
     
     
         12 . The method of  claim 9  wherein the imaging comprises positron emission tomography (PET) imaging and optionally, simultaneous or sequential magnetic resonance imaging (MRI) or computed tomography (CT) imaging. 
     
     
         13 . (canceled) 
     
     
         14 . (canceled) 
     
     
         15 . (canceled) 
     
     
         16 . The method of  claim 9 , wherein the radioisotope is  111 In and the bacteria or bacteriophage are labelled with a labelling agent comprising  111 In-DOTA-NHS. 
     
     
         17 . The method of  claim 16  wherein the imaging comprises single-photon emission computed tomography (SPECT) imaging and optionally, simultaneous or sequential magnetic resonance imaging (MRI) or computed tomography (CT) imaging. 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . (canceled) 
     
     
         24 . The method of  claim 1 , wherein the bacteriophage is selected for its ability to infect or for its specificity to the bacteria to be imaged. 
     
     
         25 . (canceled) 
     
     
         26 . The method of  claim 1 , wherein bacteriophage are labelled, the bacteriophage is selected from LH01-Myoviridae, LL5-Siphoviridae, T4D-Myoviridae, and LL12-Myoviridae and the bacteria to be imaged is  E. Coli  which is infected with said bacteriophage. 
     
     
         27 . (canceled) 
     
     
         28 . (canceled) 
     
     
         29 . (canceled) 
     
     
         30 . The method of  claim 1 , wherein the introducing of the radioisotope labelled bacteriophage comprises ingestion of the radioisotope labelled bacteriophage by the subject or transplanting the radioisotope labelled bacteriophage into the subject, or the radioisotope labelled bacteriophage is administered into the subject intravenously, intraarterially, intrathecally, intramuscularly, intradermally, subcutaneously, or intracavitarily. 
     
     
         31 . (canceled) 
     
     
         32 . (canceled) 
     
     
         33 . (canceled) 
     
     
         34 . (canceled) 
     
     
         35 . (canceled) 
     
     
         36 . (canceled) 
     
     
         37 . (canceled) 
     
     
         38 . (canceled) 
     
     
         39 . (canceled) 
     
     
         40 . (canceled) 
     
     
         41 . (canceled) 
     
     
         42 . (canceled) 
     
     
         43 . (canceled) 
     
     
         44 . (canceled) 
     
     
         45 . (canceled) 
     
     
         46 . (canceled) 
     
     
         47 . A method of quantitatively 3D imaging microbiota in a subject, the method comprising:
 labelling bacteria, viruses, bacteriophage or other microorganism with a radioisotope;   introducing the radioisotope labelled bacteria, viruses, bacteriophage or other microorganism into the subject;   functionally and/or structurally imaging the subject;   determining radioactivity of a biological sample from the subject; and   mapping the radioactivity of the biological sample with the images to generate a quantitative 3D image of bacteria, viruses, bacteriophage or other microorganism distribution.   
     
     
         48 . The method of  claim 47 , further comprising collecting a biological sample from the subject before and/or after introducing the radioisotope labelled bacteria, viruses, bacteriophage or other microorganism. 
     
     
         49 . The method of  claim 48 , further comprising determining the radioactivity of the biological sample and an average number of radioisotope labels per bacterial cell, virus, bacteriophage, or other microorganism after introducing the radioisotope labelled bacteria, viruses, bacteriophage or other microorganism. 
     
     
         50 . The method of  claim 49 , wherein the radioactivity of the biological sample is determined using a calibrated radioactive counting detector. 
     
     
         51 . The method of  claim 50 , further comprising combining one or more images resulting from the imaging, and the radioactivity per bacterial cell, virus, bacteriophage, or other microorganism, to generate a 3D image of the number of bacteria, virus, bacteriophage or other microorganism per voxel. 
     
     
         52 . The method of  claim 47 , wherein the biological sample is a stool sample and the imaged bacteria, viruses, bacteriophage, or other microorganisms are, respectively, gut bacteria, gut viruses, gut bacteriophage or other gut microorganisms. 
     
     
         53 . The method of  claim 52 , further comprising segmenting the generated 3D image to identify the gut of the subject and to determine the number and location of radioisotope labelled gut microbiota in the gut of the subject. 
     
     
         54 . The method of  claim 47 , wherein the biological sample is one or more of a urine sample, a blood sample, and a saliva sample. 
     
     
         55 . The method of  claim 54 , further comprising segmenting the generated 3D image to identify a region of interest external to a gut of the subject and to determine the number and location of radioisotope labelled microbiota in the region of interest. 
     
     
         56 . The method of  claim 49 , wherein the biological sample is analyzed to determine the kind and/or number of bacteria present using a) next generation sequencing and/or b) NMR relaxometry, by placing the biological sample in slow water exchange. 
     
     
         57 . The method of  claim 56 , further comprising combining the number and kind of bacteria with the one or more images resulting from the imaging to determine the radioactivity of the bacteria, virus, bacteriophage or other microorganism in the biological sample and the radioactivity per bacterium. 
     
     
         58 . A method of imaging microbiota in a gut of a subject, the method comprising:
 labelling gut bacteria, gut viruses, gut bacteriophage, or other gut microorganism with a radioisotope;   introducing the radioisotope labelled gut bacteria, gut viruses, gut bacteriophage, or other gut microorganism into the subject; and   functionally and/or structurally imaging the subject.   
     
     
         59 . The method of  claim 58 , further comprising:
 isolating the gut bacteria, gut viruses, gut bacteriophages or other gut microorganism from fecal material from the subject or from another subject.   
     
     
         60 . The method of  claim 58 , further comprising:
 mixing the radioisotope labeled gut bacteria, gut viruses, gut bacteriophage, or other gut microorganism into fecal material prior to introduction into the subject.   
     
     
         61 . The method of  claim 1 , wherein the functionally and/or structurally imaging the subject provides a first image, further comprising, after functionally and/or structurally imaging the subject:
 selecting a bacteriophage specific to the labelled bacteria and administering said bacteriophage to the subject;
 functionally and/or structurally imaging the subject a second time, to provide a second image; 
 comparing said first image and said second image, 
 where differences between the first image and the second image are indicative of a location of the bacteria. 
   
     
     
         62 . The method of  claim 1 , wherein the functionally and/or structurally imaging the subject provides a second image, further comprising, before labelling the bacteriophage with the isotope:
 introducing bacteria into the subject;   wherein the bacteriophage is selected for its specificity to the bacteria.   
     
     
         63 . A method of imaging microbiota in a subject, the method comprising:
 functionally and/or structurally imaging the subject, to obtain a first image;   introducing a manganese dependent bacteria into the subject; and   functionally and/or structurally imaging the subject again, to obtain a second image;   comparing the first image and the second image, wherein changes in imaging indicate location of the bacteria.   
     
     
         64 . The method of  claim 63 , wherein the manganese dependent bacteria is mixed with fecal matter before introduction into the subject. 
     
     
         65 . The method of  claim 63 , wherein the functional and/or structural imaging is through MRI and the first image and the second image are R2/R2* images. 
     
     
         66 . The method of  claim 59 , further comprising:
 mixing the radioisotope labeled gut bacteria, gut viruses, gut bacteriophage, or other gut microorganism into fecal material prior to introduction into the subject.